5ue5 - Revision history

OCA at 07:28, 1 May 2024

OCA — Wed, 01 May 2024 07:28:15 GMT

←Older revision		Revision as of 07:28, 1 May 2024
Line 1:		Line 1:

	==proMMP-7 with heparin octasaccharide bound to the catalytic domain==		==proMMP-7 with heparin octasaccharide bound to the catalytic domain==
-	<StructureSection load='5ue5' size='340' side='right'caption='[[5ue5~~]], [[NMR_Ensembles_of_Models \| 16 NMR models~~]]' scene=''>	+	<StructureSection load='5ue5' size='340' side='right'caption='[[5ue5]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ue5]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UE5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5UE5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ue5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UE5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UE5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=IDS:2-O-SULFO-ALPHA-L-IDOPYRANURONIC+ACID'>IDS</scene>, <scene name='pdbligand=SGN:N,O6-DISULFO-GLUCOSAMINE'>SGN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene~~></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2mze\|2mze]], [[5ue2\|5ue2]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=IDS:2-O-SULFO-ALPHA-L-IDOPYRANURONIC+ACID'>IDS</scene>, <scene name='pdbligand=SGN:N,O6-DISULFO-GLUCOSAMINE'>SGN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MMP7, MPSL1, PUMP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5ue5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ue5 OCA], [https://pdbe.org/5ue5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ue5 RCSB], [https://www.ebi.ac.uk/pdbsum/5ue5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ue5 ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Matrilysin Matrilysin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.23 3.4.24.23] </span></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ue5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ue5 OCA], [~~http~~://pdbe.org/5ue5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ue5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ue5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ue5 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/MMP7_HUMAN MMP7_HUMAN]] Degrades casein, gelatins of types I, III, IV, and V, and fibronectin. Activates procollagenase.<ref>PMID:2550050</ref>	+	[https://www.uniprot.org/uniprot/MMP7_HUMAN MMP7_HUMAN] Degrades casein, gelatins of types I, III, IV, and V, and fibronectin. Activates procollagenase.<ref>PMID:2550050</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Heparan sulfate proteoglycans activate the matrix metalloproteinase-7 zymogen (proMMP-7) and recruit it in order to shed proteins from cell surfaces. This occurs in uterine and mammary epithelia, bacterial killing, lung healing, and tumor cell signaling. Basic tracks on proMMP-7 recognize polyanionic heparin, according to nuclear magnetic resonance and mutations disruptive of maturation. Contacts and proximity measurements guided docking of a heparin octasaccharide to proMMP-7. The reducing end fits into a basic pocket in the pro-domain while the chain continues toward the catalytic domain. Another oligosaccharide traverses a basic swath remote on the catalytic domain and inserts its reducing end into a slot formed with the basic C terminus. This latter association appears to support allosteric acceleration of proteolysis. The modes of binding account for extended, heterogeneous assemblies of proMMP-7 with heparinoids during maturation and for bridging to pro-alpha-defensins and proteoglycans. These associations support proteolytic release of activities at epithelial cell surfaces.	+
-		+
-	Glycan Activation of a Sheddase: Electrostatic Recognition between Heparin and proMMP-7.,Fulcher YG, Prior SH, Masuko S, Li L, Pu D, Zhang F, Linhardt RJ, Van Doren SR Structure. 2017 Jul 5;25(7):1100-1110.e5. doi: 10.1016/j.str.2017.05.019. Epub, 2017 Jun 22. PMID:28648610<ref>PMID:28648610</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5ue5" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 28:		Line 17:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Matrilysin]]~~	+	[[Category: Fulcher YG]]
-	~~[[Category: Doren, S R.Van]]~~	+	[[Category: Linhardt RJ]]
-	[[Category: Fulcher~~, Y G~~]]	+	[[Category: Prior SH]]
-	[[Category: Linhardt~~, R J~~]]	+	[[Category: Van Doren SR]]
-	[[Category: Prior~~, S H~~]]	+
-	[[Category: ~~Allosteric effector site]]~~	+
-	~~[[Category: Enzyme complex with heparin oligosaccharide]]~~	+
-	~~[[Category: Glycan complex with protein]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Zymogen~~]]	+

OCA at 09:15, 1 January 2020

OCA — Wed, 01 Jan 2020 09:15:33 GMT

←Older revision		Revision as of 09:15, 1 January 2020
Line 1:		Line 1:

	==proMMP-7 with heparin octasaccharide bound to the catalytic domain==		==proMMP-7 with heparin octasaccharide bound to the catalytic domain==
-	<StructureSection load='5ue5' size='340' side='right' caption='[[5ue5]], [[NMR_Ensembles_of_Models \| 16 NMR models]]' scene=''>	+	<StructureSection load='5ue5' size='340' side='right'caption='[[5ue5]], [[NMR_Ensembles_of_Models \| 16 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ue5]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UE5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UE5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ue5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UE5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UE5 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=IDS:2-O-SULFO-ALPHA-L-IDOPYRANURONIC+ACID'>IDS</scene>, <scene name='pdbligand=SGN:N,O6-DISULFO-GLUCOSAMINE'>SGN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=IDS:2-O-SULFO-ALPHA-L-IDOPYRANURONIC+ACID'>IDS</scene>, <scene name='pdbligand=SGN:N,O6-DISULFO-GLUCOSAMINE'>SGN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2mze\|2mze]], [[5ue2\|5ue2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2mze\|2mze]], [[5ue2\|5ue2]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MMP7, MPSL1, PUMP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Matrilysin Matrilysin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.23 3.4.24.23] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Matrilysin Matrilysin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.23 3.4.24.23] </span></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ue5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ue5 OCA], [http://pdbe.org/5ue5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ue5 RCSB], [http://www.ebi.ac.uk/pdbsum/5ue5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ue5 ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ue5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ue5 OCA], [http://pdbe.org/5ue5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ue5 RCSB], [http://www.ebi.ac.uk/pdbsum/5ue5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ue5 ProSAT]</span></td></tr>
Line 20:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 5ue5" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ue5" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Matrix metalloproteinase 3D structures\|Matrix metalloproteinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Matrilysin]]		[[Category: Matrilysin]]
	[[Category: Doren, S R.Van]]		[[Category: Doren, S R.Van]]

OCA at 09:43, 27 September 2017

OCA — Wed, 27 Sep 2017 09:43:45 GMT

←Older revision		Revision as of 09:43, 27 September 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ue5 is ~~ON HOLD~~	+	==proMMP-7 with heparin octasaccharide bound to the catalytic domain==
		+	<StructureSection load='5ue5' size='340' side='right' caption='[[5ue5]], [[NMR_Ensembles_of_Models \| 16 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ue5]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UE5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UE5 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=IDS:2-O-SULFO-ALPHA-L-IDOPYRANURONIC+ACID'>IDS</scene>, <scene name='pdbligand=SGN:N,O6-DISULFO-GLUCOSAMINE'>SGN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2mze\|2mze]], [[5ue2\|5ue2]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Matrilysin Matrilysin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.23 3.4.24.23] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ue5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ue5 OCA], [http://pdbe.org/5ue5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ue5 RCSB], [http://www.ebi.ac.uk/pdbsum/5ue5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ue5 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MMP7_HUMAN MMP7_HUMAN]] Degrades casein, gelatins of types I, III, IV, and V, and fibronectin. Activates procollagenase.<ref>PMID:2550050</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Heparan sulfate proteoglycans activate the matrix metalloproteinase-7 zymogen (proMMP-7) and recruit it in order to shed proteins from cell surfaces. This occurs in uterine and mammary epithelia, bacterial killing, lung healing, and tumor cell signaling. Basic tracks on proMMP-7 recognize polyanionic heparin, according to nuclear magnetic resonance and mutations disruptive of maturation. Contacts and proximity measurements guided docking of a heparin octasaccharide to proMMP-7. The reducing end fits into a basic pocket in the pro-domain while the chain continues toward the catalytic domain. Another oligosaccharide traverses a basic swath remote on the catalytic domain and inserts its reducing end into a slot formed with the basic C terminus. This latter association appears to support allosteric acceleration of proteolysis. The modes of binding account for extended, heterogeneous assemblies of proMMP-7 with heparinoids during maturation and for bridging to pro-alpha-defensins and proteoglycans. These associations support proteolytic release of activities at epithelial cell surfaces.

-	~~Authors~~: ~~Fulcher, Y.G~~., Prior, S~~.H.~~, ~~Linhardt~~, ~~R.J.~~, Van Doren~~, S~~.R.	+	Glycan Activation of a Sheddase: Electrostatic Recognition between Heparin and proMMP-7.,Fulcher YG, Prior SH, Masuko S, Li L, Pu D, Zhang F, Linhardt RJ, Van Doren SR Structure. 2017 Jul 5;25(7):1100-1110.e5. doi: 10.1016/j.str.2017.05.019. Epub, 2017 Jun 22. PMID:28648610<ref>PMID:28648610</ref>

-	~~Description: proMMP-7 with heparin octasaccharide bound to~~ the ~~catalytic domain~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Fulcher~~, Y.G]]	+	<div class="pdbe-citations 5ue5" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Prior~~, ~~S.H~~]]	+	== References ==
-	[[Category: Linhardt, R.J]]	+	<references/>
-	[[Category: ~~Van Doren~~, S.R]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Matrilysin]]
		+	[[Category: Doren, S R.Van]]
		+	[[Category: Fulcher, Y G]]
		+	[[Category: Linhardt, R J]]
		+	[[Category: Prior, S H]]
		+	[[Category: Allosteric effector site]]
		+	[[Category: Enzyme complex with heparin oligosaccharide]]
		+	[[Category: Glycan complex with protein]]
		+	[[Category: Hydrolase]]
		+	[[Category: Zymogen]]

OCA at 18:58, 15 March 2017

OCA — Wed, 15 Mar 2017 18:58:32 GMT

←Older revision		Revision as of 18:58, 15 March 2017
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Fulcher, Y.G]]		[[Category: Fulcher, Y.G]]
-	[[Category: Linhardt, R.J]]
	[[Category: Prior, S.H]]		[[Category: Prior, S.H]]
		+	[[Category: Linhardt, R.J]]
	[[Category: Van Doren, S.R]]		[[Category: Van Doren, S.R]]

OCA at 14:23, 9 March 2017

OCA — Thu, 09 Mar 2017 14:23:33 GMT

←Older revision		Revision as of 14:23, 9 March 2017
Line 3:		Line 3:
	The entry 5ue5 is ON HOLD		The entry 5ue5 is ON HOLD

-	Authors: ~~Yan G.~~Fulcher, ~~Stephen H~~.Prior, ~~Robert J~~.Linhardt, ~~Steven~~ R.Van Doren	+	Authors: Fulcher, Y.G., Prior, S.H., Linhardt, R.J., Van Doren, S.R.

	Description: proMMP-7 with heparin octasaccharide bound to the catalytic domain		Description: proMMP-7 with heparin octasaccharide bound to the catalytic domain
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Yan G.~~Fulcher, ~~Stephen H.Prior, Robert J~~.Linhardt, ~~Steven~~ R.Van Doren]]	+	[[Category: Fulcher, Y.G]]
		+	[[Category: Linhardt, R.J]]
		+	[[Category: Prior, S.H]]
		+	[[Category: Van Doren, S.R]]

OCA at 16:32, 1 February 2017

OCA — Wed, 01 Feb 2017 16:32:01 GMT

←Older revision		Revision as of 16:32, 1 February 2017
Line 3:		Line 3:
	The entry 5ue5 is ON HOLD		The entry 5ue5 is ON HOLD

-	Authors: Yan G. Fulcher, Stephen H. Prior, Robert J. Linhardt, Steven R. Van Doren	+	Authors: Yan G.Fulcher, Stephen H.Prior, Robert J.Linhardt, Steven R.Van Doren

	Description: proMMP-7 with heparin octasaccharide bound to the catalytic domain		Description: proMMP-7 with heparin octasaccharide bound to the catalytic domain
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Yan G. Fulcher, Stephen H. Prior, Robert J. Linhardt, Steven R. Van Doren]]	+	[[Category: Yan G.Fulcher, Stephen H.Prior, Robert J.Linhardt, Steven R.Van Doren]]

OCA: Protected "5ue5" [edit=sysop:move=sysop]

OCA — Wed, 04 Jan 2017 15:44:05 GMT

Protected "5ue5" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:44, 4 January 2017

OCA: New page: '''Unreleased structure''' The entry 5ue5 is ON HOLD Authors: Yan G. Fulcher, Stephen H. Prior, Robert J. Linhardt, Steven R. Van Doren Description: proMMP-7 with heparin octasaccharid...

OCA — Wed, 04 Jan 2017 15:44:04 GMT

New page: '''Unreleased structure''' The entry 5ue5 is ON HOLD Authors: Yan G. Fulcher, Stephen H. Prior, Robert J. Linhardt, Steven R. Van Doren Description: proMMP-7 with heparin octasaccharid...

New page

'''Unreleased structure'''

The entry 5ue5 is ON HOLD

Authors: Yan G. Fulcher, Stephen H. Prior, Robert J. Linhardt, Steven R. Van Doren

Description: proMMP-7 with heparin octasaccharide bound to the catalytic domain
[[Category: Unreleased Structures]]
[[Category: Yan G. Fulcher, Stephen H. Prior, Robert J. Linhardt, Steven R. Van Doren]]